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OPENSEQ.org
Msi172-qsem covariation
Genes: A B A+B
Length: 83 83 153
Sequences: 97 429 68
Seq/Len: 1.17 5.17 0.44
MirrorTree (Pazo et al. 2001) 0.53
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.02 0.17 0.37
2 0.02 0.28 0.41
5 0.02 0.29 0.41
10 0.03 0.30 0.41
20 0.03 0.31 0.41
100 0.04 0.32 0.41
∞ 0.12 0.37 0.41
Paired alignment generation
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Sequence A E-value:
Iterations:
Sequence B E-value:
Iterations:
Δgene MSA
Figure 1: The effect of Δgene on ratio of paralogs in the genome for each gene, and the number of sequences in the resulting joined alignment. Figure 2: Distribution of Δgene across all genomes. Figure 3: Current parameters. You can use the form to adjust the parameters and resubmit the job!
GREMLIN results (Scaled_score > 1):
Figure 4: The darker and larger the blue dots, the higher strength in coevolution. 		Inter Residue pairs sorted by strength in coevolution signal:
i j Scaled Score Prob I_Prob
34_F 23_F 2.36 0.94 0.78
37_R 31_D 1.90 0.78 0.46
42_Q 58_A 1.69 0.66 0.30
23_R 24_T 1.53 0.55 0.19
14_Q 39_E 1.48 0.51 0.17
14_Q 28_R 1.36 0.42 0.11
33_E 80_L 1.27 0.36 0.08
49_L 14_S 1.24 0.34 0.07
69_D 62_V 1.16 0.29 0.05
12_D 32_A 1.12 0.26 0.05
41_F 5_V 1.09 0.24 0.04
23_R 46_V 1.07 0.23 0.04
19_Y 28_R 1.05 0.23 0.03
69_D 81_F 1.04 0.22 0.03
29_G 74_T 1.02 0.21 0.03
19_Y 78_K 1.02 0.21 0.03
18_S 27_M 1.02 0.21 0.03
46_R 79_E 1.01 0.20 0.03
63_L 33_S 1.00 0.20 0.03
42_Q 54_E 0.99 0.20 0.03
41_F 36_D 0.98 0.19 0.03
74_G 32_A 0.98 0.19 0.03
32_W 78_K 0.98 0.19 0.03
17_K 54_E 0.98 0.19 0.03
72_Q 55_P 0.97 0.18 0.02
50_E 70_N 0.93 0.17 0.02
65_R 8_E 0.93 0.17 0.02
35_L 57_R 0.91 0.16 0.02
27_R 81_F 0.91 0.16 0.02
14_Q 36_D 0.91 0.16 0.02
62_E 56_E 0.90 0.16 0.02
14_Q 41_E 0.89 0.15 0.02
78_R 45_L 0.89 0.15 0.02
38_N 22_H 0.89 0.15 0.02
16_E 6_Q 0.89 0.15 0.02
35_L 58_A 0.88 0.15 0.02
38_N 74_T 0.88 0.15 0.02
14_Q 47_L 0.88 0.15 0.02
62_E 36_D 0.87 0.14 0.01
30_W 62_V 0.87 0.14 0.01
79_K 11_W 0.86 0.14 0.01
72_Q 30_L 0.86 0.14 0.01
36_R 76_G 0.85 0.14 0.01
47_H 61_A 0.85 0.14 0.01
35_L 28_R 0.85 0.14 0.01
75_L 36_D 0.84 0.14 0.01
9_D 35_D 0.84 0.14 0.01
50_E 82_A 0.84 0.13 0.01
34_F 16_T 0.84 0.13 0.01
45_C 82_A 0.84 0.13 0.01
34_F 6_Q 0.83 0.13 0.01
9_D 55_P 0.83 0.13 0.01
51_H 46_V 0.82 0.13 0.01
40_A 54_E 0.82 0.13 0.01
45_C 63_R 0.82 0.12 0.01
46_R 83_R 0.82 0.12 0.01
41_F 47_L 0.81 0.12 0.01
41_F 62_V 0.81 0.12 0.01
80_L 12_S 0.81 0.12 0.01
58_W 36_D 0.81 0.12 0.01
31_A 80_L 0.81 0.12 0.01
10_W 34_A 0.81 0.12 0.01
80_L 14_S 0.81 0.12 0.01
25_L 10_P 0.81 0.12 0.01
71_T 81_F 0.81 0.12 0.01
28_R 58_A 0.80 0.12 0.01
31_A 51_P 0.80 0.12 0.01
Figure 5: The i (protein A) and j (protein B) are positions as given in the query sequences.

Scaled Score = raw_score/average(raw_scores)
Prob = P(contact | scaled_score, seq/len)
I_Prob = P(contact | scaled_score, seq/len, top_inter_score)
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